Contacts of the helix formed by residues 452 - 456 (chain B) in PDB entry 1ZY7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 452 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451B CYS* 1.3 76.6 - - - +
453B ASP* 1.3 67.6 + - - -
454B ALA 3.3 1.3 - - - -
455B ARG* 2.9 15.7 + - - +
456B ILE* 3.3 17.7 - - - +
481B ARG* 4.0 6.3 - - - -
490B THR* 3.6 24.7 + - - +
515B SER* 3.7 13.0 - - - -
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Residues in contact with ASP 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B GLY* 1.3 71.4 - - - -
454B ALA* 1.3 63.0 + - - +
455B ARG 3.1 0.9 + - - -
456B ILE* 3.2 16.7 + - - +
477B ARG* 3.5 5.2 - - - +
478B GLY* 2.8 35.4 + - - -
479B GLN* 4.1 6.5 + - - +
481B ARG* 4.1 6.7 - - - +
515B SER* 4.6 0.8 + - - -
517B SER* 3.4 6.6 + - - -
518B ASP* 5.0 0.4 + - - -
558B ARG* 2.7 47.8 + - - +
559B ALA* 3.4 24.5 - - + +
563B ARG* 3.9 20.3 - - - +
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Residues in contact with ALA 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B SER* 3.2 23.6 + - - +
450B PRO* 3.8 7.6 - - + +
453B ASP* 1.3 77.1 - - - +
455B ARG* 1.3 56.4 + - - +
457B PHE* 3.5 18.0 - - - -
517B SER* 3.0 18.6 + - - +
550B LEU 4.9 0.2 - - - +
552B HIS 5.9 0.2 + - - -
555B HIS* 3.7 14.2 - - - +
556B LEU* 3.7 21.0 + - + -
559B ALA* 3.4 18.3 - - + +
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Residues in contact with ARG 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B VAL* 5.4 3.8 - - - +
375B THR* 5.8 2.0 + - - -
394B HIS* 6.0 1.0 + - - -
396B GLU* 5.2 1.8 + - - -
448B THR* 3.7 18.1 + - - +
449B SER* 2.8 33.0 + - - +
450B PRO* 3.8 8.1 + - - +
451B CYS* 3.3 32.5 - - - +
452B GLY 2.9 10.4 + - - +
454B ALA* 1.3 79.9 - - - +
456B ILE* 1.3 65.3 + - + +
457B PHE* 3.2 20.5 + - + +
488B GLU* 4.9 7.9 + - - +
489B GLY* 5.5 3.6 - - - -
550B LEU* 3.7 32.2 - - + +
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Residues in contact with ILE 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B GLY* 3.3 24.7 - - - +
453B ASP* 3.2 18.7 + - - +
454B ALA 3.4 1.2 - - - -
455B ARG* 1.3 80.8 - - + +
457B PHE* 1.3 53.3 + - - +
474B ARG* 3.4 26.7 - - - +
477B ARG* 2.7 43.7 + - + -
481B ARG* 3.6 42.8 - - - +
490B THR* 5.1 0.9 - - - +
558B ARG* 4.1 4.2 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il